Package: decontX 1.5.0

Yuan Yin

decontX: Decontamination of single cell genomics data

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Authors:Yuan Yin [aut, cre], Masanao Yajima [aut], Joshua Campbell [aut]

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decontX.pdf |decontX.html✨
decontX/json (API)
NEWS

# Install 'decontX' in R:
install.packages('decontX', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:decontX-1.3.0(bioc 3.20)decontX-1.2.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecellbayesian

4.66 score 23 scripts 394 downloads 11 exports 228 dependencies

Last updated 23 days agofrom:b7aed7b70c. Checks:OK: 1 NOTE: 4 WARNING: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64WARNINGOct 31 2024
R-4.4-mac-aarch64WARNINGOct 31 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64WARNINGOct 31 2024
R-4.3-mac-aarch64WARNINGOct 31 2024

Exports:decontProdecontXdecontXcountsdecontXcounts<-plotBoxByClusterplotDecontXContaminationplotDecontXMarkerExpressionplotDecontXMarkerPercentageplotDensityretrieveFeatureIndexsimulateContamination

Dependencies:abindaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblusterbslibcachemCairocallrcaToolsceldacheckmatecirclizecliclueclustercodetoolscolorspacecombinatcommonmarkComplexHeatmapcowplotcpp11crayoncrosstalkcurldata.tabledbscanDelayedArraydeldirdescdigestdistributionaldoParalleldotCall64dplyrdqrngedgeRenrichRevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelggridgesGlobalOptionsglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphinlineIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevalleidenlifecyclelimmalistenvlmtestlocfitloomagrittrMASSMatrixMatrixGenericsmatrixStatsMCMCprecisionmemoisemetapodmgcvmimeminiUImunsellnlmenumDerivopensslparallellypatchworkpbapplypheatmappillarpkgbuildpkgconfigplotlyplyrpngpolyclipposteriorprocessxprogressrpromisespspurrrQuickJSRR6raggRANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressRcppTOMLreshape2reticulaterjsonrlangrmarkdownROCRrprojrootRSpectrarstanrstantoolsrsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscattermorescransctransformscuttleSeuratSeuratObjectshapeshinySingleCellExperimentsitmosnowsourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsStanHeadersstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstensortensorAtextshapingtibbletidyrtidyselecttinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrWriteXLSxfunxtableXVectoryamlzlibbioczoo

Decontamination of single cell protein expression data with DecontPro

Yuan Yin, Joshua Campbell

Rendered fromdecontPro.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-10-21
Started: 2023-02-22

Decontamination of ambient RNA in single-cell genomic data with DecontX

Shiyi (Iris) Yang, Zhe Wang, Yuan Yin, Joshua Campbell

Rendered fromdecontX.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-10-21
Started: 2023-03-01

Readme and manuals

Help Manual

Help pageTopics
The 'decontX' package.decontX-package
Call Stan variational bayes for inference.call_stan_vb
Process Stan output..process_stan_vb_out
Decontaminate using decontProdecontPro decontPro,ANY-method decontPro,Seurat-method decontPro,SingleCellExperiment-method
Contamination estimation with decontXdecontX decontX,ANY-method decontX,SingleCellExperiment-method
Get or set decontaminated counts matrixdecontXcounts decontXcounts,SingleCellExperiment-method decontXcounts<- decontXcounts<-,SingleCellExperiment-method
Fast normalization for numeric matrixfastNormProp
Fast normalization for numeric matrixfastNormPropLog
Fast normalization for numeric matrixfastNormPropSqrt
get row and column indices of none zero elements in the matrixnonzero
Boxplot of features grouped by cell typeplotBoxByCluster
Plots contamination on UMAP coordinatesplotDecontXContamination
Plots expression of marker genes before and after decontaminationplotDecontXMarkerExpression
Plots percentage of cells cell types expressing markersplotDecontXMarkerPercentage
Density of each ADT, raw counts overlapped with decontaminated countsplotDensity
Retrieve row index for a set of featuresretrieveFeatureIndex
Simulate contaminated count matrixsimulateContamination